Noi/NOTES/2014-4-14: Difference between revisions
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>Noi (Created page with "= gDNA extraction of cell cultures (Song' samples) = : '''Sample info.''' :: - Three vials for day 0 ESCs (ESCd0.1, ESCd0.2,ESCd0.3) :: - Three vials for definitive endoderm c...") |
>Noi mNo edit summary |
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: - For accuracy, the concentration will be based on Qubit measurement | : - For accuracy, the concentration will be based on Qubit measurement | ||
= Amplified DNA samples form Illumina = | |||
'''4-14-2014''' | |||
* Received 8 additional amplified DNA samples from Xuyu Cai | |||
* No information of sample was provide only 5ul for each one and concentration ~200ng/ul | |||
* I added more H2O to bring volume to 12ul, transfered samples to 8-tube strip with individual cap, and re-quantified concentration with Qubit ssDNA HS assay | |||
==== Qubit dsDNA assay HS results ==== | |||
{| {{table}} class = wikitable | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''Conc. in the Qubit''' | |||
| align="center" style="background:#f0f0f0;"|'''Unit''' | |||
| align="center" style="background:#f0f0f0;"|'''uL used''' | |||
| align="center" style="background:#f0f0f0;"|'''Dilution''' | |||
| align="center" style="background:#f0f0f0;"|'''Sample conc. (ng/ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''Total volume''' | |||
| align="center" style="background:#f0f0f0;"|'''Total amount (ng)''' | |||
|- | |||
| #1||173||ng/mL||1||200||34.6||12||415.2 | |||
|- | |||
| #2||152||ng/mL||1||200||30.4||12||364.8 | |||
|- | |||
| #3||199||ng/mL||1||200||39.9||12||478.8 | |||
|- | |||
| #4||207||ng/mL||1||200||41.4||12||496.8 | |||
|- | |||
| #5||108||ng/mL||1||200||21.6||12||259.2 | |||
|- | |||
| #6||154||ng/mL||1||200||30.9||12||370.8 | |||
|- | |||
| #7||181||ng/mL||1||200||36.1||12||433.2 | |||
|- | |||
| #8||172||ng/mL||1||200||34.4||12||412.8 | |||
|} | |||
'''5-06-2014''' | |||
* Received ~30ul of polymerase with property similar to Amplitaq Stoffel fragment. Conc. 3U/ul. She is not allowed to provide any further info. of this enzyme. |
Latest revision as of 14:28, 8 May 2014
gDNA extraction of cell cultures (Song' samples)[edit]
- Sample info.
- - Three vials for day 0 ESCs (ESCd0.1, ESCd0.2,ESCd0.3)
- - Three vials for definitive endoderm cells (DEd3.1,DEd3.2,DEd3.3)
- - Two vials for naive cells. (naiveESC.1, naiveESC.2)
- - Extract gDNA using DNeasy Blood & Tissue Kit (QIAGEN) with RNaseA treatment and followed the instruction of the kit
- - Elute DNA with 200ul AE buffer (single elution)
- - Measure concentration with Nanodrop (ND) and Qubit dsDNA HS assay
Qubit dsDNA HS assay and Nanodrop (ND) quantification[edit]
Sample | Conc. in the Qubit | Unit | uL used | Dilution | Sample conc. (ng/ul) | Yields in 200ul (ug) | conc. By ND (ng/ul) | 260/280 | 260/230 |
ESCd0.1 | 201 | ng/mL | 1 | 200 | 40.30 | 8.06 | 53.15 | 1.92 | 1.88 |
ESCd0.2 | 280 | ng/mL | 1 | 200 | 56.00 | 11.20 | 76.53 | 1.88 | 1.81 |
ESCd0.3 | 430 | ng/mL | 1 | 200 | 86.00 | 17.20 | 107.13 | 1.91 | 1.94 |
DEd3.1 | 170 | ng/mL | 1 | 200 | 34.00 | 6.80 | 44.91 | 1.91 | 2.07 |
DEd3.2 | 188 | ng/mL | 1 | 200 | 37.70 | 7.54 | 47.82 | 1.91 | 2.02 |
DEd3.3 | 129 | ng/mL | 1 | 200 | 25.70 | 5.14 | 34.79 | 1.84 | 1.85 |
naiveESC.1 | 132 | ng/mL | 1 | 200 | 26.30 | 5.26 | 39.75 | 1.86 | 1.55 |
naiveESC.2 | 150 | ng/mL | 1 | 200 | 30.00 | 6.00 | 44.82 | 1.86 | 1.52 |
- - For accuracy, the concentration will be based on Qubit measurement
Amplified DNA samples form Illumina[edit]
4-14-2014
- Received 8 additional amplified DNA samples from Xuyu Cai
- No information of sample was provide only 5ul for each one and concentration ~200ng/ul
- I added more H2O to bring volume to 12ul, transfered samples to 8-tube strip with individual cap, and re-quantified concentration with Qubit ssDNA HS assay
Qubit dsDNA assay HS results[edit]
Sample | Conc. in the Qubit | Unit | uL used | Dilution | Sample conc. (ng/ul) | Total volume | Total amount (ng) |
#1 | 173 | ng/mL | 1 | 200 | 34.6 | 12 | 415.2 |
#2 | 152 | ng/mL | 1 | 200 | 30.4 | 12 | 364.8 |
#3 | 199 | ng/mL | 1 | 200 | 39.9 | 12 | 478.8 |
#4 | 207 | ng/mL | 1 | 200 | 41.4 | 12 | 496.8 |
#5 | 108 | ng/mL | 1 | 200 | 21.6 | 12 | 259.2 |
#6 | 154 | ng/mL | 1 | 200 | 30.9 | 12 | 370.8 |
#7 | 181 | ng/mL | 1 | 200 | 36.1 | 12 | 433.2 |
#8 | 172 | ng/mL | 1 | 200 | 34.4 | 12 | 412.8 |
5-06-2014
- Received ~30ul of polymerase with property similar to Amplitaq Stoffel fragment. Conc. 3U/ul. She is not allowed to provide any further info. of this enzyme.